Issues

Issues

• to_polygons() on labels is not pixel-exact: half-pixel shift, cut corners, filled holes, chunk-dependent output

  Bug

  scverse/spatialdata#1301 · opened on Nov 6, 2026

• Py3.14: fsspec[s3] can resolve ancient s3fs 0.3.5; suggest s3fs>=2024.1 floor

  scverse/spatialdata#1293 · opened on Oct 28, 2026
  1

• Affine transformations are written to disk different from how they are stored in memory

  Enhancement

  scverse/spatialdata#1284 · opened on Oct 23, 2026
  5

• bounding_box_query slows down with string cell IDs in newest spatialdata release

  Bug

  scverse/spatialdata#1279 · opened on Oct 19, 2026

• bounding_box_query(filter_table=True) restores dropped categories but not their colors in uns

  scverse/spatialdata#1271 · opened on Oct 9, 2026

• SpatialData 0.8.0 permits Zarr versions that do not provide ArrayNotFoundError

  scverse/spatialdata#1256 · opened on Sep 22, 2026

• aggregate(values, by=<labels with no non-background instance>) raises a misleading 'regions do not match' error

  scverse/spatialdata#1250 · opened on Sep 13, 2026

• aggregate(values, by=<multiscale labels>) crashes with AttributeError despite DataTree being a declared input type

  scverse/spatialdata#1249 · opened on Sep 13, 2026

• bounding_box_query(filter_table=True) crashes if the SpatialData object contains an orphan table

  scverse/spatialdata#1248 · opened on Sep 13, 2026

• Collection of minor issues found by an automated bug hunt (validation edge cases, misleading errors, small inefficiencies)

  scverse/spatialdata#1244 · opened on Sep 11, 2026

• repr(sdata) reports the parquet row count for any points element that shares backing files, even after lazy filtering

  scverse/spatialdata#1243 · opened on Sep 11, 2026

• Joins on an element with duplicated index values duplicate rows (inner/right) instead of erroring

  scverse/spatialdata#1242 · opened on Sep 11, 2026

• concatenate(): orphan tables crash the dict form; a generator input gives a misleading error

  scverse/spatialdata#1241 · opened on Sep 11, 2026

• validate_table_in_spatialdata: the instance-key dtype-mismatch TypeError can never fire (dtype is str)

  scverse/spatialdata#1240 · opened on Sep 11, 2026

• unpad_raster() (public API) raises 'Please report this bug' on any all-zero raster

  scverse/spatialdata#1239 · opened on Sep 11, 2026

• Multi-box bounding_box_query works on elements but crashes on a SpatialData object (TypeError: Unsupported type list)

  scverse/spatialdata#1238 · opened on Sep 11, 2026

• write_element(name, overwrite=True) can never overwrite an existing element, even purely in-memory tables/shapes

  scverse/spatialdata#1237 · opened on Sep 11, 2026

• rasterize(labels, value_key=...) crashes for categorical table columns and for labels absent from the table

  scverse/spatialdata#1236 · opened on Sep 11, 2026

• to_polygons(labels) turns a label containing a hole into an invalid MultiPolygon with the hole counted as area

  scverse/spatialdata#1235 · opened on Sep 11, 2026
  2

• spatialdata.models.force_2d() silently drops interior rings (holes) of polygons

  scverse/spatialdata#1234 · opened on Sep 11, 2026

• get_extent(circles, exact=True) (the default) is wrong for anisotropic/shearing transformations, while exact=False is right

  scverse/spatialdata#1233 · opened on Sep 11, 2026

• bounding_box_query on circles ignores the radius (only the centre is tested), polygon_query does not

  scverse/spatialdata#1232 · opened on Sep 11, 2026

• A failing aggregate() leaves the internal __ones_column / __areas_column on the user's shapes element

  scverse/spatialdata#1231 · opened on Sep 11, 2026

• aggregate(image, by=labels) crashes when the labels have no background (no zero pixels)

  scverse/spatialdata#1230 · opened on Sep 11, 2026

• TableModel rejects int8/uint8 instance-key columns although the error message promises 'uint equivalents' (breaks aggregate/to_circles on uint8 labels)

  scverse/spatialdata#1229 · opened on Sep 11, 2026